Well, very unsurprising one uses 3.3V, the other 5V. Thus the available output voltage on the pins of the 3.3V Arduino is just 3.3V. That shouldn't come as a big surprise either. Also the 3.3V runs at 8MHz, the 5V at 16MHz. For this reason, make sure you select the correct version in the IDE before compiling, otherwise many things depending on timings will behave strangely.

If you want to interface to most common stuff, use the 5V version. It is electrically and from the software side fully compatible with the Arduino Duemilanove. The 3.3V Version is more for setups where you run off batteries and where you interface with 3.3V devices only. It's electrically more compatible with the Lilypads, which also use 3.3V and 8MHz processors.

In the end, the decision is up to you which one fits your requirement best. And don't foget to get the correct FTDI USB-to-TTL converter. Those exist in 5V and 3.3V preconfigured (or you need to solder / open a bridge if you want to switch).